diff --git a/qmk_cli/subcommands/setup.py b/qmk_cli/subcommands/setup.py
index 83a3f3b..2bab3f0 100644
--- a/qmk_cli/subcommands/setup.py
+++ b/qmk_cli/subcommands/setup.py
@@ -104,4 +104,4 @@ def setup(cli):
         if cli.args.yes:
             doctor_command.append('-y')
 
-        cli.run(doctor_command, stdin=None, capture_output=False)
+        cli.run(doctor_command, stdin=None, capture_output=False, cwd=cli.args.home)